WDR75

WD repeat domain 75, the group of WD repeat domain containing|UTPa subcomplex

Basic information

Region (hg38): 2:189441446-189475552

Links

ENSG00000115368 ∙ NCBI:84128 ∙ ∙ HGNC:25725 ∙ Uniprot:Q8IWA0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WDR75 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR75 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	0	0

Variants in WDR75

This is a list of pathogenic ClinVar variants found in the WDR75 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-189441515-G-T		not specified	Uncertain significance (Apr 12, 2023)
2-189448405-T-C		not specified	Uncertain significance (Jun 07, 2023)
2-189448463-A-C		not specified	Uncertain significance (Feb 22, 2023)
2-189451876-A-G		not specified	Uncertain significance (Nov 10, 2021)
2-189451887-A-G		not specified	Uncertain significance (Dec 01, 2022)
2-189455392-T-C		not specified	Uncertain significance (Feb 02, 2022)
2-189457332-C-T		not specified	Uncertain significance (May 06, 2022)
2-189457368-A-G		not specified	Uncertain significance (Jun 17, 2024)
2-189458803-C-T		not specified	Uncertain significance (Mar 07, 2023)
2-189458851-T-C		not specified	Uncertain significance (Aug 09, 2021)
2-189459361-T-C		not specified	Uncertain significance (Mar 20, 2023)
2-189459392-A-G		not specified	Uncertain significance (Aug 19, 2023)
2-189459401-T-G		not specified	Uncertain significance (Nov 21, 2022)
2-189462504-G-A		not specified	Uncertain significance (Sep 16, 2021)
2-189462508-G-T		not specified	Uncertain significance (Oct 12, 2022)
2-189462529-G-T		not specified	Uncertain significance (Aug 16, 2022)
2-189462532-G-A		not specified	Uncertain significance (Dec 19, 2023)
2-189462614-T-A		not specified	Uncertain significance (Oct 26, 2022)
2-189463956-T-C		not specified	Uncertain significance (Apr 12, 2024)
2-189465085-A-G		not specified	Uncertain significance (May 02, 2024)
2-189465128-T-C		not specified	Uncertain significance (Mar 31, 2024)
2-189465187-C-G		not specified	Uncertain significance (Oct 02, 2023)
2-189465203-C-T		not specified	Uncertain significance (May 08, 2023)
2-189466505-A-G		not specified	Uncertain significance (Sep 16, 2021)
2-189466557-A-G		not specified	Uncertain significance (Aug 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR75	protein_coding	protein_coding	ENST00000314761	21	34133

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000171	1.00	125659	1	88	125748	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	353	423	0.834	0.0000205	5451
Missense in Polyphen		89	129.78	0.68578		1690
Synonymous	-0.352	161	155	1.04	0.00000813	1505
Loss of Function	4.07	17	47.2	0.360	0.00000227	595

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000240	0.000239
Ashkenazi Jewish	0.00378	0.00378
East Asian	0.0000547	0.0000544
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.0000547	0.0000544
South Asian	0.000548	0.000457
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ribosome biogenesis factor. Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre- ribosomal RNA transcription by RNA polymerase I. {ECO:0000269|PubMed:17699751}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: -1.22
• rvis_percentile_EVS: 5.6

Haploinsufficiency Scores

• pHI: 0.427
• hipred: Y
• hipred_score: 0.704
• ghis: 0.655

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.716

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Wdr75

Zebrafish Information Network

• Gene name: wdr75
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: rRNA processing;positive regulation of transcription by RNA polymerase I;positive regulation of rRNA processing
• Cellular component: nucleoplasm;nucleolus
• Molecular function: RNA binding